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This page was generated on 2024-06-11 15:40 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 813/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicRanges 1.57.0  (landing page)
Hervé Pagès
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/GenomicRanges
git_branch: devel
git_last_commit: d8c95f2
git_last_commit_date: 2024-04-30 14:34:23 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    ERROR  skipped
palomino4Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
merida1macOS 12.7.4 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson1macOS 13.6.6 Ventura / arm64  OK    ERROR  skippedskipped


BUILD results for GenomicRanges on palomino4

To the developers/maintainers of the GenomicRanges package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GenomicRanges.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: GenomicRanges
Version: 1.57.0
Command: chmod a+r GenomicRanges -R && F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data GenomicRanges
StartedAt: 2024-06-09 19:14:43 -0400 (Sun, 09 Jun 2024)
EndedAt: 2024-06-09 19:18:31 -0400 (Sun, 09 Jun 2024)
EllapsedTime: 228.3 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
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###
### Running command:
###
###   chmod a+r GenomicRanges -R && F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data GenomicRanges
###
##############################################################################
##############################################################################


* checking for file 'GenomicRanges/DESCRIPTION' ... OK
* preparing 'GenomicRanges':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'GenomicRangesIntroduction.Rmd' using rmarkdown
--- finished re-building 'GenomicRangesIntroduction.Rmd'

--- re-building 'ExtendingGenomicRanges.Rnw' using Sweave
texify: major issue: User/administrator updates are out-of-sync.
--- finished re-building 'ExtendingGenomicRanges.Rnw'

--- re-building 'GRanges_and_GRangesList_slides.Rnw' using Sweave
Warning in .merge_two_Seqinfo_objects(x, y) :
  The 2 combined objects have no sequence levels in common. (Use
  suppressWarnings() to suppress this warning.)
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts,
    colCummaxs, colCummins, colCumprods, colCumsums, colDiffs,
    colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs,
    colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles,
    colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates,
    colVarDiffs, colVars, colWeightedMads, colWeightedMeans,
    colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls,
    rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts,
    rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs,
    rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs,
    rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles,
    rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates,
    rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans,
    rowWeightedMedians, rowWeightedSds, rowWeightedVars

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")',
    and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Loading required package: Rsamtools
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
texify: major issue: User/administrator updates are out-of-sync.
--- finished re-building 'GRanges_and_GRangesList_slides.Rnw'

--- re-building 'GenomicRangesHOWTOs.Rnw' using Sweave

Attaching package: 'txdbmaker'

The following objects are masked from 'package:GenomicFeatures':

    UCSCFeatureDbTableSchema, browseUCSCtrack,
    getChromInfoFromBiomart, makeFDbPackageFromUCSC,
    makeFeatureDbFromUCSC, makePackageName, makeTxDb,
    makeTxDbFromBiomart, makeTxDbFromEnsembl, makeTxDbFromGFF,
    makeTxDbFromGRanges, makeTxDbFromUCSC, makeTxDbPackage,
    makeTxDbPackageFromBiomart, makeTxDbPackageFromUCSC,
    supportedMiRBaseBuildValues, supportedUCSCFeatureDbTables,
    supportedUCSCFeatureDbTracks, supportedUCSCtables

Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... Warning in .get_cds_IDX(mcols0$type, mcols0$phase) :
  The "phase" metadata column contains non-NA values for features
  of type exon. This information was ignored.
OK
Loading required package: BiocFileCache
Loading required package: dbplyr

Attaching package: 'AnnotationHub'

The following object is masked from 'package:Biobase':

    cache

loading from cache
Loading required package: limma

Attaching package: 'limma'

The following object is masked from 'package:DESeq2':

    plotMA

The following object is masked from 'package:BiocGenerics':

    plotMA

Loading required package: BSgenome
Loading required package: BiocIO
Loading required package: rtracklayer

Attaching package: 'rtracklayer'

The following object is masked from 'package:BiocIO':

    FileForFormat

The following object is masked from 'package:AnnotationHub':

    hubUrl


Attaching package: 'KEGGgraph'

The following object is masked from 'package:graphics':

    plot

The following object is masked from 'package:base':

    plot

trying URL 'https://rest.kegg.jp/get/hsa05210/kgml'
downloaded 32 KB


Error: processing vignette 'GenomicRangesHOWTOs.Rnw' failed with diagnostics:
 chunk 56 (label = cancer_5) 
Error : subscript contains invalid names

--- failed re-building 'GenomicRangesHOWTOs.Rnw'

--- re-building 'Ten_things_slides.Rnw' using Sweave
Error in x$.self$finalize() : attempt to apply non-function
Warning: call dbDisconnect() when finished working with a connection
texify: major issue: User/administrator updates are out-of-sync.
--- finished re-building 'Ten_things_slides.Rnw'

SUMMARY: processing the following file failed:
  'GenomicRangesHOWTOs.Rnw'

Error: Vignette re-building failed.
Execution halted